Many structural defects and strain fields develop during the preparation of thin films and nanostructures, with their origins being at the atomic level1,2. Sensitively detecting these subtle features with high sensitivity and resolution, and their influence3 on electronic, thermal, and mechanical properties, remains challenging. Scanning probe microscopy (SPM) methods4 have been useful to measure such properties locally, but standard measurements are not well suited to detect the small changes in lattice parameters that accompany strain and disorder, and large scale imaging of the associated electronic states are prohibitive. Here we show that local thermopower measurements can yield high sensitivity large scale imaging of structural disorder in epitaxial graphene, which is not observable in the standard SPM topographic images. The thermopower measurement acts to amplify the variations in the local density of states at the Fermi-level, giving high differential contrast in thermoelectric signals. Using this new imaging technique, we discovered a defect-mediated dimensional evolution of strain-response patterns in epitaxial graphene with increasing thickness. Our findings suggest that local-thermopower is a new means for exploring Fermi-energy phenomena resulting from structural features or quantum confinement.